5HIX

Cocrystal structure of an anti-parallel DNA G-quadruplex and a tetra-Quinoline Foldamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Multivalent Interactions between an Aromatic Helical Foldamer and a DNA G-Quadruplex in the Solid State.

Mandal, P.K.Baptiste, B.Langlois d'Estaintot, B.Kauffmann, B.Huc, I.

(2016) Chembiochem 17: 1911-1914

  • DOI: https://doi.org/10.1002/cbic.201600281
  • Primary Citation of Related Structures:  
    5HIX

  • PubMed Abstract: 

    Quinoline-based oligoamide foldamers have been identified as a potent class of ligands for G-quadruplex DNA. Their helical structure is thought to target G-quadruplex loops or grooves and not G-tetrads. We report a co-crystal structure of the antiparallel hairpin dimeric DNA G-quadruplex (G 4 T 4 G 4 ) 2 with tetramer 1-a helically folded oligo-quinolinecarboxamide bearing cationic side chains-that is consistent with this hypothesis. Multivalent foldamer-DNA interactions that modify the packing of (G 4 T 4 G 4 ) 2 in the solid state are observed.


  • Organizational Affiliation

    INSERM, IECB, US001), 2 rue Escarpit, 33600, Pessac, France.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
Dimeric G-quadruplex
A, B
12synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
61Q
Query on 61Q

Download Ideal Coordinates CCD File 
G [auth A]4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-nitroquinolin-2-yl]carbonyl}amino)quinolin-2-yl]carbonyl}amino)quinolin-2-yl]carbonyl}amino)quinoline-2-carboxylic acid
C52 H52 N12 O11
PDPDTUNURBJNEI-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.701α = 90
b = 31.701β = 90
c = 97.373γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilFranceERC-2012-AdG-320892

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description